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Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks

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Computational Cell Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1819))

Abstract

Spatial analysis of functional enrichment (SAFE) is a systematic quantitative approach for annotating large biological networks. SAFE detects network regions that are statistically overrepresented for functional groups or quantitative phenotypes of interest, and provides an intuitive visual representation of their relative positioning within the network. In doing so, SAFE determines which functions cocluster in a network, which parts of the network they are associated with and how they are potentially related to one another.

Here, I provide a detailed stepwise description of how to perform a SAFE analysis. As an example, I use SAFE to annotate the genome-scale genetic interaction similarity network from Saccharomyces cerevisiae with Gene Ontology (GO) biological process terms. In addition, I show how integrating GO with chemical genomic data in SAFE can recapitulate known modes of action of chemical compounds and potentially identify novel drug mechanisms.

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Author information

Authors and Affiliations

  1. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA

    Anastasia Baryshnikova

  2. Calico Life Sciences LLC, South San Francisco, CA, 94080, USA

    Anastasia Baryshnikova

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  1. Anastasia Baryshnikova
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Correspondence to Anastasia Baryshnikova .

Editor information

Editors and Affiliations

  1. NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

    Louise von Stechow

  2. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

    Alberto Santos Delgado

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Baryshnikova, A. (2018). Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks. In: von Stechow, L., Santos Delgado, A. (eds) Computational Cell Biology. Methods in Molecular Biology, vol 1819. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8618-7_12

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  • DOI: https://doi.org/10.1007/978-1-4939-8618-7_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8617-0

  • Online ISBN: 978-1-4939-8618-7

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